Lung cancer is the greatest cause of cancer-related deaths of men and women in the United States. Recent appreciation of the specific types of lung cancer has led to more effective, tailored therapies. One of the major types is lung squamous cell carcinoma (LSCC), which is a heterogeneous disease with a wide range of clinical outcomes. Several recent studies identified LSCC subtypes using gene expression microarrays, but there has been no attempt to validate these results, which is a prerequisite if LSCC subtypes are to be used in clinical decisions or future research. One of the principal drivers of the wildly altered tumor gene expression is genomic copy number or the gain and loss of chromosomal segments. Our core hypothesis is LSCC has reproducible molecular subtypes defined by alterations in gene expression and copy number, which represent distinct clinical diseases and biological processes. In preliminary work, our laboratory analyzed published raw microarray data from multiple independent cohorts and demonstrated that four LSCC subtypes can be reliably recognized. To pursue our core hypothesis, we have assembled a new independent LSCC cohort (UNC). We hypothesize the four a priori LSCC subtypes are robust biological diseases and as such will exist in the independent UNC cohort. The UNC cohort will be assayed by gene expression microarrays. UNC cohort subtype will be predicted by historical cohorts and validated with internal UNC predictions. Our preliminary analysis of inferring copy number differences by cytoband differential gene expression demonstrated several subtype-specific regions: 3q22-29, 8q24, and 18q12. We hypothesize that these and additional regions will differentiate the LSCC subtypes. To test this hypothesis, we will computationally detect UNC cohort genomic copy number, measured by SNP microarrays. To translate our results into a clinical application, we will develop an immunohistochemical assay that can predict LSCC subtype of clinical tissue specimens. We will then use our assay to predict LSCC subtype in a large independent cohort and evaluate whether LSCC subtypes have distinct clinical courses, such as survival, metastasis patterns, and response to chemotherapy. PUBLIC HEALTH RELEVANCE: A new molecular LSCC classification may help explain the wide variety of clinical outcomes in this disease and provide a basis for new specialized therapies. The assay developed through this proposal will allow LSCC subtype identification in clinical specimens and is a step towards a routine clinical diagnostic. Subtype-specific genomic copy number aberrations may contribute to etiological models of LSCC.